Biology subjects

Rozen, D.

Publications and source records attributed to Rozen, D..

15 recordsLinked to original sources

bioRxiv2025

The influence of heteroresistance, growth and antibiotic selection in shaping the invasion dynamics of colistin resistant Pseudomonas aeruginosa

Heteroresistance, where a small subpopulation of phenotypically resistant cells coexists within an otherwise susceptible population, plays a critical role in bacterial survival during antibiotic exposure. Yet, its influence on the invasion success of genetically resistant strains remains poorly understood. In this study, we investigate the influence of bacterial heteroresistance, growth, and antibiotic selection on the outcome of an invasion experiment. We quantified the invasion dynamics of a bioluminescent colistin-resistant Pseudomonas aeruginosa strain across a colistin concentration gradient during co-culture with colistin-susceptible clinical P. aeruginosa isolates with varying levels of heteroresistance. The observed variation in heteroresistance and fitness of the clinical isolates allowed investigation of the impact of these factors on invasion dynamics. We hypothesized that fitter isolates would limit invasion through competitive exclusion, while heteroresistant isolates, despite their growth costs, may serve as reservoirs for resistance evolution under antibiotic selection. Our results show that in antibiotic-free conditions, faster-growing isolates competitively excluded the colistin resistant invader while isolates with high levels of heteroresistance failed to do so. This competitive landscape shifted with increasing colistin concentration, giving the invader a fitness advantage that peaked around 2-4xMIC of the clinical isolate. The shift in the landscape over the colistin gradient might further have been influenced by the presence of heteroresistance in the clinical isolates. These findings reveal how both heteroresistance and competitive exclusion shapes invasion dynamics. Understanding these interactions is critical for redesigning treatment strategies that minimize ecological opportunities for resistant strains to establish and expand.

microbiology↗

bioRxiv2025

Antibiotic production reduces the cost of resource cheaters in Streptomyces coelicolor

Soil is a competitive environment containing a variety of resources used for bacterial growth. Complex polysaccharides, like chitin or starch, require the secretion of enzymes that degrade these resources into smaller units before they can be consumed. However, exoenzymes and the products they create are public goods, meaning they can be used by competitors, called "cheaters", who benefit from public goods even if they do not produce enzymes themselves. Here, we test the hypothesis that antibiotics produced by Streptomyces are used to privatize public goods by restricting access to resource cheaters. Using experiments with Streptomyces coelicolor and Bacillus subtilis, we first show that B. subtilis cheating significantly reduces S. coelicolor fitness on complex medium (starch) but not on a simple carbon source (maltose) which does not require exoenzyme secretion. Next, we show that antibiotics produced by S. coelicolor markedly increase fitness against resource cheaters, despite evidence that antibiotic production is metabolically costly. Finally, we find that the benefits of antibiotic production and the costs of resource cheating are both higher during growth on lower resource concentrations. Our results provide novel insights into the context-dependent costs and benefits of antibiotic secretion in Streptomyces and highlight the role of resource complexity and concentration in mediating competitive strategies in bacteria.

evolutionary biology↗

bioRxiv2025

Being bigger is better: Size-dependent advantages of plasmodial fusion in a multinucleated slime mould

Larger body size often enhances survival and reproduction. While most organisms grow to achieve larger sizes, some can rapidly increase size through fusion. Fusion decisions are influenced by genetic relatedness and environmental factors, balancing potential benefits and costs. In Physarum polycephalum, a multinucleated slime mould, fusion is thought to occur mainly between genetically identical or highly related individuals. However, the frequency of fusion among close relatives, and the drivers and benefits of fusion, remain unclear. This study explored fusion frequency, morphology, and benefits among clonal and closely related individuals of Physarum. We also assessed the impact of abiotic stress on fusion and whether genetic relatedness between fusion partners influences survival during exposure to stress. Our results revealed variation in fusion frequency and morphology among different plasmodial lines and pairs of close relatives. Abiotic stress increased fusion rates between both clonal and compatible non-clonal pairs. However, the benefits of fusion did not depend on the whether fusion occurred between clones or non-clones. These findings demonstrate plasmodial fusion provides size-related survival benefits. Furthermore, the promotion of fusion in stressful conditions highlights its adaptive role in responding to environmental challenges. Collectively, these results underscore the evolutionary importance of fusion in Physarum, shaping its ecological success and resilience. Competing Interests StatementThe authors declare no competing financial interests.

evolutionary biology↗

bioRxiv2024

Using BONCAT To Dissect The Proteome Of S. aureus Persisters

Bacterial persisters are a subpopulation of cells that exhibit a transient non-susceptible phenotype in the presence of bactericidal antibiotic concentrations. This phenotype can lead to the survival and regrowth of bacteria after treatment, resulting in relapse of infections. As such, it is also a contributing factor to antibacterial resistance. Multiple processes are believed to cause persister formation, yet identifying the proteins expressed during the induction of the persister state has been difficult, because the persister-state is rare, transient and does not lead to genetic changes. In this study, we used Bio-Orthogonal Non-Canonical Amino Acid Tagging (BONCAT) to label, and retrieve, the proteome expressed during the persister state for different strains of methicillin-resistant Staphylococcus aureus. After incubating antibiotic-exposed bacteria with the methionine ortholog L-azidohomoalanine to label the proteins of persister cells, we retrieved labeled proteins using click chemistry-pulldown methodology. Analysis of the retrieved proteome fraction of Methicillin resistant Staphylococcus aureus (MRSA) and Vancomycin resistant Staphylococcus aureus (VRSA) under challenge with {beta}-lactam and fluoroquinolone antibiotics with Label Free Quantification - Liquid chromatography mass spectrometry (LFQ-LCMS) based proteomics reveals the upregulation of proteins involved in stringent response, cell wall biosynthesis, purine metabolism, ppGpp biosynthesis, two component systems (TCS), lipid metabolism, ABC transporters, D-alanine biosynthesis and L-proline degradation. Conversely, we observed a decline of proteins associated with amino acid biosynthesis and degradation, protein biosynthesis, protein modification, and carbohydrate metabolism, among others. These findings indicate that modification of translational activity in persister cells enables bacterial cells to induce an active defense to survive antibiotic pressure.

microbiology↗

bioRxiv2024

A family of lanthipeptides with anti-phage function

Bacteria synthesize natural products to adapt to their environment, where phage-bacteria interactions play a crucial role in bacterial ecology. Although a few natural products have been shown to protect bacteria from phage infection, the prevalence and diversity of chemical anti-phage defense remain largely unexplored. Here, we uncover a novel family of over 2000 lanthipeptide biosynthetic gene clusters from Actinobacteria that participate in anti-phage defense, which we named lanthiphages. Lanthiphages colocalize with other anti-phage systems in defense islands. We demonstrate that native lanthiphage expression protects the model strain Streptomyces coelicolor against diverse phages. Heterologous expression of four additional lanthiphage pathways shows that the anti-phage function is conserved across this family of biosynthetic gene clusters. Finally, we demonstrate that lanthiphage expression leads to the production of a novel compound and alters phage transcription. Our findings highlight that biosynthetic gene clusters with anti-phage functions can be successfully identified through genomic analysis. This work paves the way for the systematic mining of anti-phage natural products, which could constitute a novel reservoir of antiviral drugs.

microbiology↗

bioRxiv2024

Bacterial heterozygosity promotes survival under multidrug selection

Although bacterial cells typically contain a single chromosome, some species are naturally polyploid and carry multiple copies of their chromosome. Polyploid chromosomes can be identical or heterogeneous, the latter giving rise to bacterial heterozygosity. While the benefits of heterozygosity are well studied in eukaryotes, its consequences in bacteria are unknown. Here we examine this question in the context of antibiotic resistance to understand how bacterial heterozygosity affects bacterial survival. Using a cell wall deficient model system in the actinomycete Kitasatospora viridifaciens, we found that heterozygous cells containing different chromosomes expressing different antibiotic resistance markers persist across a broader range of antibiotic concentrations. Recombinant cells containing the same resistance genes on a single chromosome also survive these conditions, but these cells pay a significant fitness cost due to constitutive expression of these genes. By contrast, heterozygous cells mitigate these costs by flexibly adjusting the ratio of their different chromosomes, thereby allowing rapid responses in temporally and spatially variable environments. Our results provide evidence that bacterial heterozygosity can increase adaptive plasticity in bacterial cells, in a similar manner to the evolutionary benefits provided by multicopy plasmids in bacteria. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/593358v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@b7a6e8org.highwire.dtl.DTLVardef@12edf40org.highwire.dtl.DTLVardef@4323fborg.highwire.dtl.DTLVardef@1ef6416_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIHeterozygotic bacterial cells (polyploid with multiple chromosome types) can persist across a wider range of conditions than homozygotic cells. C_LIO_LIHeterozygous cells can adaptively adjust chromosomal frequencies in response to external conditions C_LIO_LIFlexibly adjusting chromosome ratios enables heterozygous cells to mitigate the costs of antibiotic resistance and allows rapid responses to temporally and spatially variable environments C_LIO_LIHeterozygosity can increase adaptive plasticity in bacterial cells, in a similar manner to the evolutionary benefits provided by multicopy plasmids. C_LI

microbiology↗

bioRxiv2024

Factors that influence the caste ratio in a bacterial division of labour

Colonies of the bacteria Streptomyces coelicolor divide labour between cells that specialize on growth and sporulation and cells that specialize on antibiotic production. This division of labour arises due to costly chromosome deletions in the antibiotic overproducers. However, little is known about when and where these mutations occur or whether their frequency - which we liken to the caste ratio in social insects - is phenotypically plastic. To elucidate changes in the proportions of specialized cells (measured as the mutation frequency), we sampled S. coelicolor colonies grown under different conditions. Temporally, mutation frequency increased linearly with colony age and size. Spatially, mutations accumulated disproportionately in the colony center, despite greater growth and sporulation at the periphery. Exposing colonies to sub-inhibitory concentrations of some antibiotics, a competitive cue in Streptomyces, increased mutation frequencies. Finally, direct competition with other Streptomyces that naturally produce antibiotics increased mutation frequencies, while also increasing spore production. Our findings provide insights into the intrinsic and environmental factors driving division of labor in Streptomyces colonies by showing that mutation frequencies are dynamic and responsive to the competitive environment. These results show that chromosome deletions are phenotypically plastic and suggest that Streptomyces can flexibly adjust their caste ratio.

evolutionary biology↗

bioRxiv2021

Reversible bacteriophage resistance by shedding the bacterial cell wall

Phages are highly abundant in the environment and a major threat for bacteria. Therefore, bacteria have evolved sophisticated defense systems to withstand phage attacks. Here, we describe a previously unknown mechanism by which mono- and diderm bacteria survive infection with diverse lytic phages. Phage exposure leads to a rapid and near complete conversion of walled cells to a cell wall-deficient state, which remain viable in osmoprotective conditions and can revert to the walled state. While shedding the cell wall dramatically reduces the number of progeny phages produced by the host, it does not always preclude phage infection. Altogether, these results show that the formation of cell wall-deficient cells prevents complete eradication of the bacterial population and suggest that cell wall-deficiency may limit the efficacy of phage therapy, especially in highly osmotic environments or when used together with antibiotics that target the cell wall.

microbiology↗

bioRxiv2021

Generating heterokaryotic cells via bacterial cell-cell fusion

Cell-cell fusion is fundamentally important for tissue repair, virus transmission, and genetic recombination, among other functions. Fusion has been mainly studied in eukaryotic cells and lipid vesicles, while cell-cell fusion in bacteria is less well characterized, due to the cell wall acting as a fusion-limiting barrier. Here we use cell wall-deficient bacteria to investigate the dynamics of cell fusion in bacteria that replicate without their cell wall. Stable, replicating cells containing differently labeled chromosomes were successfully obtained from fusion. We find that the rate of cell-cell fusion depends on the fluidity of cell membranes. Furthermore, we show that not only the efficiency but also the specificity of cell-cell fusion can be controlled via a pair of synthetic membrane-associated lipopeptides. Our results provide a molecular handle to understand and control cell-cell fusion to generate heterokaryotic cells, which was an important step in the evolution of protocells and of increasing importance for the design of synthetic cells.

microbiology↗

bioRxiv2020

Manganese complex Br increases antibiotic sensitivity in multidrug resistant Streptococcus pneumoniae

The emergence of multidrug-resistance (MDR) in Streptococcus pneumoniae clones and non-vaccine serotypes is of increasing concern, necessitating the development of novel treatment strategies. Here, we determined the efficacy of the Mn complex [Mn(CO)3(tpa-{kappa}3N)]Br against MDR S. pneumoniae strains. Our data showed that [Mn(CO)3(tpa-{kappa}3N)]Br has in vitro and in vivo antibacterial activity and has the potential to be used in combination with currently available antibiotics to increase their effectiveness against MDR S. pneumoniae.

microbiology↗

bioRxiv2019

Antibiotic production is organized by a division of labour in Streptomyces

One of the hallmark behaviors of social groups is division of labour, where different group members become specialized to carry out complementary tasks. By dividing labour, cooperative groups of individuals increase their efficiency, thereby raising group fitness even if these specialized behaviors reduce the fitness of individual group members. Here we provide evidence that antibiotic production in colonies of the multicellular bacterium Streptomyces coelicolor is coordinated by a division of labour. We show that S. coelicolor colonies are genetically heterogenous due to massive amplifications and deletions to the chromosome. Cells with gross chromosomal changes produce an increased diversity of secondary metabolites and secrete significantly more antibiotics; however, these changes come at the cost of dramatically reduced individual fitness, providing direct evidence for a trade-off between secondary metabolite production and fitness. Finally, we show that colonies containing mixtures of mutant strains and their parents produce significantly more antibiotics, while colony-wide spore production remains unchanged. Our work demonstrates that by generating mutants that are specialized to hyper-produce antibiotics, streptomycetes reduce the colony-wide fitness costs of secreted secondary metabolites while maximizing the yield and diversity of these products.

evolutionary biology↗

bioRxiv2017

Fitness effects and transmission of phoretic nematodes of the burying beetle, Nicrophorus vespilloides

O_LINicrophorus vespilloides is a cosmopolitan social beetle that rears its offspring on decomposing carrion. Wild beetles are frequently associated with two types of macrobial symbionts, mites and nematodes.\nC_LIO_LIAlthough these organisms are believed to be phoretic commensals that harmlessly use beetles as a means of transfer between carcasses, the role of these symbionts on N. vespilloides fitness is poorly understood. Here we show that nematodes have significant negative effects on beetle fitness across a range of worm densities and also quantify the density-dependent transmission of worms between mating individuals and from parents to offspring.\nC_LIO_LIUsing field-caught beetles, we provide the first report of a new nematode symbiont in N. vespilloides, most closely related to Rhabditoides regina, and show that worm densities are highly variable across individuals isolated from nature but do not differ between males and females. Next, by inoculating mating females with increasing densities of nematodes, we show that worm infections significantly reduce brood size, larval survival and larval mass, and also eliminate the trade-off between brood size and larval mass. Finally, we show that nematodes are efficiently transmitted between mating individuals and from mothers to larvae, directly and indirectly via the carcass, and that worms persist through pupation.\nC_LIO_LIThese results show that the phoretic nematode R. regina can be highly parasitic to burying beetles but can nevertheless persist because of efficient mechanisms of intersexual and intergenerational transmission.\nC_LIO_LIPhoretic species are exceptionally common and may cause significant harm to their hosts, even though they rely on these larger species for transmission to new resources. However, this harm may be inevitable and unavoidable if transmission of phoretic symbionts requires nematode proliferation. It will be important to determine the generality of our result for other phoretic associates of animals.\nC_LI

ecology↗

bioRxiv2017

Gut microbiota in the burying beetle, Nicrophorus vespilloides, provide colonization resistance against larval bacterial pathogens

Carrion beetles, Nicrophorus vespilloides, are reared on decomposing vertebrate carrion where larvae are exposed to high-density populations of carcass-derived bacteria. We previously showed that larvae do not become colonized with these bacteria, but instead are colonized with the gut microbiome of their parents. These results suggested that bacteria in the beetle microbiome outcompete the carcass derived species for colonization of the larval gut. Here we test this hypothesis directly and quantify the fitness consequences of colonization of the Nicrophorus larval gut with different bacterial symbionts, including the insect pathogen Serratia marcescens. First, we show that beetles colonized by their endogenous microbiome produce significantly heavier broods than those colonized with carcass-bacteria. Next, we show that bacteria from the endogenous microbiome, including Providencia rettgeri and Morganella morganii, are better colonizers of the beetle gut and can outcompete non-endogenous species, including S. marcescens and Escherichia coli, during in vivo competition. Finally, we find that Providencia and Morganella provide beetles with colonization resistance against Serratia and thereby reduce Serratia-induced larval mortality during co-inoculation. Importantly, this effect is eliminated in larvae first colonized by Serratia, suggesting that while competition within the larval gut is strongly determined by priority effects, these effects are less important for Serratia-induced mortality. Our work supports the idea that bacterial gut symbionts provide direct benefits to Nicrophorus larvae by outcompeting potential bacterial pathogens. They further suggest that one benefit of parental care in Nicrophorus vespilloides is the social transmission of the microbiome from caring parents to their offspring.

microbiology↗

bioRxiv2016

Colonization and transmission of the gut microbiotaof the burying beetle, Nicrophorus vespolloides,through development

Carrion beetles in the genus Nicrophorus rear their offspring on decomposing carcasses where larvae are exposed to a diverse microbiome of decomposer bacteria. Parents coat the carcass with antimicrobial secretions prior to egg hatch (defined as Pre-Hatch care) and also feed regurgitated food, and potentially bacteria, to larvae throughout development (defined as Full care). Here we partition the roles of pre- and post-hatch parental care in the transmission and persistence of culturable symbiotic bacteria to larvae. Using three treatment groups (Full-Care, Pre-Hatch care only, and No Care), we found that larvae receiving Full-Care are predominantly colonized by bacteria resident in the maternal gut, while larvae receiving No Care are colonized exclusively with bacteria from the carcass. More importantly, larvae receiving only Pre-Hatch care were also predominantly colonized by maternal bacteria; this result indicates that parental treatment of the carcass, including application of bacteria to the carcass surface, is sufficient to ensure symbiont transfer even in the absence of direct larval feeding. Later in development, we found striking evidence that pupae undergo a aposymbiotic stage, after which they are recolonized at eclosion with bacteria shed in the moulted larval cuticle and on the wall of the pupal chamber. Our results clarify the importance of pre-hatch parental care for symbiont transmission in Nicrophorus vespilloides, and suggest that these bacteria successfully outcompete decomposer bacteria during larval and pupal gut colonization.\n\nImportanceHere we examine the origin and persistence of the culturable gut microbiota of larvae in the burying beetle Nicrophorus vespilloides. This insect is particularly interesting for this study because larvae are reared on decomposing vertebrate carcasses where they are exposed to high-densities of carrion-decomposing microbes. Larvae also receive extensive parental care in the form of carcass preservation and direct larval feeding. We find that parents transmit their gut bacteria to larvae both directly, through regurgitation, and indirectly via their effects on the carcass. In addition, we find that larvae become aposymbiotic during pupation, but are recolonized from bacteria shed onto the insect cuticle before adult eclosion. Our results highlight the diverse interactions between insect behavior and development on microbiota composition. They further indicate that strong competitive interactions mediate the bacterial composition of Nicrophorus larvae, suggesting that the bacterial communities of these insects may be highly coevolved with their host species.

ecology↗

bioRxiv2016

Crosstalk and eavesdropping among quorum sensing peptide signals that regulate bacteriocin production in Streptococcus pneumoniae

Quorum sensing (QS), where bacteria secrete and respond to chemical signals to coordinate population-wide behaviors, has revealed that bacteria are highly social. Here, we investigate how diversity in QS signals and receptors can modify social interactions controlled by the QS system regulating bacteriocin secretion in Streptococcus pneumoniae, encoded by the blp operon (bacteriocin-like peptide). Analysis of 4 096 pneumococcal genomes detected nine blp QS signals (BlpC) and five QS receptor groups (BlpH). Imperfect concordance between signals and receptors suggested widespread social interactions between cells, specifically eavesdropping (where cells respond to signals that they do not produce) and crosstalk (where cells produce signals that non-clones detect). This was confirmed in vitro by measuring the response of reporter strains containing each of six different blp QS receptors to cognate and non-cognate peptides. Assays between pneumococcal colonies grown adjacent to one another provided further evidence that crosstalk and eavesdropping occur at endogenous levels of signal secretion. Finally, simulations of QS strains producing bacteriocins revealed that eavesdropping can be evolutionarily beneficial even when the affinity for non-cognate signals is very weak. Our results highlight that social interactions can mediate intraspecific competition among bacteria and reveal that competitive interactions can be modified by polymorphic QS systems.

microbiology↗